xenial (1) maf2anchors.pl.1.gz

NAME

       maf2anchors -- Converts maf files into Murasaki anchor sets

SYNOPSIS

       maf2anchors <file.maf>

OPTIONS

       --prefix=<S>
           use <S> as a prefix for output file names (otherwise uses <file.maf>)

       --rifts=<I>
           allow up to <I> rifts.

       --fakeseqs
           generate fake sequence length files and sequence stubs based on sequence length data in MAF file

       --trust
           trust the comment annotation added by TBA on the second line of the file (if present) that it lists
           tree used in the alignment and all of the sequences involved. Defaults to on. use --notrust to
           distrust TBA tags (technically this data isn't part of the file format specification and is just
           crammed into comments that TBA produces, but might not be present or accurate on all MAF files, thus
           we give you the option to distrust it).

       --sort
           Sort the sequences found by --trust (so as to match the output that would have happened with
           --notrust).